Hi, I have followed this tutorial . I have finished the code for the proposed exercise: “getting a sphere between two fiducial points”. The problem is know how to write the code to get the sphere between the two fiducials but I don’t know in which class or position of the class to append my code. (I wrote “Added by me” everywhere I made a change to the original example-code to make it more searchable)
import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
ModuleOne
class ModuleOne(ScriptedLoadableModule):
“”“Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
“””
def init(self, parent):
ScriptedLoadableModule.init(self, parent)
self.parent.title = “ModuleOne” # TODO make this more human readable by adding spaces
self.parent.categories = [“Examples”]
self.parent.dependencies = []
self.parent.contributors = [“John Doe (AnyWare Corp.)”] # replace with “Firstname Lastname (Organization)”
self.parent.helpText = “”"
This is an example of scripted loadable module bundled in an extension.
It performs a simple thresholding on the input volume and optionally captures a screenshot.
“”"
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = “”"
This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.
and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
“”" # replace with organization, grant and thanks.
ModuleOneWidget
class ModuleOneWidget(ScriptedLoadableModuleWidget):
“”“Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
“””
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer)
uiWidget = slicer.util.loadUI(self.resourcePath('UI/ModuleOne.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
self.ui.inputSelector.setMRMLScene(slicer.mrmlScene)
self.ui.outputSelector.setMRMLScene(slicer.mrmlScene)
# connections
self.ui.applyButton.connect('clicked(bool)', self.onApplyButton)
self.ui.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.ui.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
#Added by me
self.observedMarkupNode = None
self.markupsObserverTag = None
self.ui.enableScreenshotsFlagCheckBox.connect("toggled(bool)", self.onEnableAutoUpdate)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
#Added by me
self.a = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode","sphere")
self.m = vtk.vtkSphereSource()
self.m.Update()
self.a.SetAndObservePolyData(self.m.GetOutput())
def cleanup(self):
pass
def onSelect(self):
self.ui.applyButton.enabled = self.ui.inputSelector.currentNode()
def onEnableAutoUpdate(self, autoUpdate):
if self.markupsObserverTag:
self.observedMarkupNode.RemoveObserver(self.markupsObserverTag)
self.observedMarkupNode = None
self.markupsObserverTag = None
if autoUpdate and self.ui.inputSelector.currentNode:
self.observedMarkupNode = self.ui.inputSelector.currentNode()
self.markupsObserverTag = self.observedMarkupNode.AddObserver(
vtk.vtkCommand.ModifiedEvent, self.onMarkupsUpdated)
def onMarkupsUpdated(self, caller=None, event=None):
self.onApplyButton()
def onApplyButton(self):
logic = ModuleOneLogic()
enableScreenshotsFlag = self.ui.enableScreenshotsFlagCheckBox.checked
imageThreshold = self.ui.imageThresholdSliderWidget.value
logic.run(self.ui.inputSelector.currentNode(), self.ui.outputSelector.currentNode(), imageThreshold, enableScreenshotsFlag)
#Added by me
self.m.Update()
ModuleOneLogic
class ModuleOneLogic(ScriptedLoadableModuleLogic):
“”“This class should implement all the actual
computation done by your module. The interface
should be such that other python code can import
this class and make use of the functionality without
requiring an instance of the Widget.
Uses ScriptedLoadableModuleLogic base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
“””
def hasImageData(self,volumeNode):
“”“This is an example logic method that
returns true if the passed in volume
node has valid image data
“””
if not volumeNode:
logging.debug(‘hasImageData failed: no volume node’)
return False
if volumeNode.GetImageData() is None:
logging.debug(‘hasImageData failed: no image data in volume node’)
return False
return True
def isValidInputOutputData(self, inputVolumeNode, outputVolumeNode):
“”“Validates if the output is not the same as input
“””
if not inputVolumeNode:
logging.debug(‘isValidInputOutputData failed: no input volume node defined’)
return False
if not outputVolumeNode:
logging.debug(‘isValidInputOutputData failed: no output volume node defined’)
return False
if inputVolumeNode.GetID()==outputVolumeNode.GetID():
logging.debug(‘isValidInputOutputData failed: input and output volume is the same. Create a new volume for output to avoid this error.’)
return False
return True
#Added by me
def setSphereRadiusAndCenter(r,c):
self.m = vtk.vtkSphereSource()
self.m.SetRadius®
self.m.SetCenter(c[0],c[1],c[2])
self.m.Update()
return
def setSphereTouchingFiducials(self):
import numpy
f = slicer.util.getNode(‘F’)
pos0 = [0,0,0]
pos1 = [0,0,0]
if f.GetNumberOfMarkups() == 2:
f.GetNthFiducialPosition(0,pos0)
f.GetNthFiducialPosition(1,pos1)
p0 = numpy.array(pos0)
p1 = numpy.array(pos1)
radius = numpy.linalg.norm(p0-p1)/2.0
center = (p0+p1)/2.0
self.setSphereRadiusAndCenter(radius,center)
else:
logging.info(‘Error: Incorrect number of fiducial points’)
def run(self, inputVolume, outputVolume, imageThreshold, enableScreenshots=0):
“”"
Run the actual algorithm
“”"
self.setSphereTouchingFiducials()
return True
class ModuleOneTest(ScriptedLoadableModuleTest):
“”"
This is the test case for your scripted module.
Uses ScriptedLoadableModuleTest base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
“”"
def setUp(self):
“”" Do whatever is needed to reset the state - typically a scene clear will be enough.
“”"
slicer.mrmlScene.Clear(0)
def runTest(self):
“”“Run as few or as many tests as needed here.
“””
self.setUp()
self.test_ModuleOne1()
def test_ModuleOne1(self):
“”" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
“”"
self.delayDisplay("Starting the test")
#
# first, get some data
#
import SampleData
SampleData.downloadFromURL(
nodeNames='FA',
fileNames='FA.nrrd',
uris='http://slicer.kitware.com/midas3/download?items=5767')
self.delayDisplay('Finished with download and loading')
volumeNode = slicer.util.getNode(pattern="FA")
logic = ModuleOneLogic()
self.assertIsNotNone( logic.hasImageData(volumeNode) )
self.delayDisplay('Test passed!')